Abstract
The major challenges in biophysical characterization of human protein–carbohydrate interactions are obtaining monodispersed preparations of human proteins that are often post-translationally modified and lack of detection of carbohydrates by traditional detection systems. Light scattering (dynamic and static) techniques offer detection of biomolecules and their complexes based on their size and shape, and do not rely on chromophore groups (such as aromatic amino acid sidechains). In this study, we utilized dynamic light scattering, analytical ultracentrifugation and small-angle X-ray scattering techniques to investigate the solution properties of a complex resulting from the interaction between a 15 kDa heparin preparation and miniagrin, a miniaturized version of agrin. Results from dynamic light scattering, sedimentation equilibrium, and sedimentation velocity experiments signify the formation of a monodisperse complex with 1:1 stoichiometry, and low-resolution structures derived from the small-angle X-ray scattering measurements implicate an extended conformation for a side-by-side miniagrin‒heparin complex.
Similar content being viewed by others
References
Campanelli JT, Gayer GG, Scheller RH (1996) Alternative RNA splicing that determines agrin activity regulates binding to heparin and alpha-dystroglycan. Development 122:1663–1672
Cohn EJ, Edsall JT (1943) Proteins, amino acids and peptides as ions and dipolar ions. Reinhold, New York
Dam J, Schuck P (2004) Calculating sedimentation coefficient distributions by direct modeling of sedimentation velocity concentration profiles. Methods Enzymol 384:185–212
Denzer AJ, Brandenberger R, Gesemann M, Chiquet M, Ruegg MA (1997) Agrin binds to the nerve-muscle basal lamina via laminin. J Cell Biol 137:671–683
Devetzis V, Daryadel A, Roumeliotis S, Theodoridis M, Wagner CA, Hettwer S, Huynh-Do U, Ploumis P, Arampatzis S (2015) C-terminal fragment of agrin (CAF): a novel marker for progression of kidney disease in iype 2 diabetics. PLoS One 10:e0143524
Garcia De La Torre J, Huertas ML, Carrasco B (2000) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 78:719–730
Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana Press, pp 571–607. https://doi.org/10.1385/1-59259-890-0:571
Gesemann M, Cavalli V, Denzer AJ, Brancaccio A, Schumacher B, Ruegg MA (1996) Alternative splicing of agrin alters its binding to heparin, dystroglycan, and the putative agrin receptor. Neuron 16:755–767
Guinier A, Fourner G (1955) Small angle scattering of X-rays. Wiley, New York
Hall DR, Harding SE, Winzor DJ (1999) On the correct analysis of low-speed sedimentation equilibrium distributions recorded by the Rayleigh interference optical system in a Beckman XL-I ultracentrifuge. Prog Colloid Polym Sci 113:62–68
Jeffrey PD, Nichol LW, Teasdale RD (1979) Studies of macromolecular heterogeneous associations involving cross-linking: a re-examination of the ovalbumin-lysozyme system. Biophys Chem 10:379–387
Kammerer RA, Schulthess T, Landwehr R, Schumacher B, Lustig A, Yurchenco PD, Ruegg MA, Engel J, Denzer AJ (1999) Interaction of agrin with laminin requires a coiled-coil conformation of the agrin-binding site within the laminin gamma1 chain. EMBO J18:6762–6770
Kawahara R, Granato DC, Carnielli CM, Cervigne NK, Oliveria CE, Rivera C, Yokoo S, Fonseca FP, Lopes M, Santos-Silva AR, Graner E, Coletta RD, Paes Leme AF (2014) Agrin and perlecan mediate tumorigenic processes in oral squamous cell carcinoma. PLoS One 9:e115004
Kim MJ, Cotman SL, Halfter W, Cole GJ (2003) The heparan sulfate proteoglycan agrin modulates neurite outgrowth mediated by FGF-2. J Neurobiol 55:261–277
Kim MJ, Liu IH, Song Y, Lee JA, Halfter W, Balice-Gordon RJ, Linney E, Cole GJ (2007) Agrin is required for posterior development and motor axon outgrowth and branching in embryonic zebrafish. Glycobiology 17:231–247
Kim N, Stiegler AL, Cameron TO, Hallock PT, Gomez AM, Huang JH, Hubbard SR, Dustin ML, Burden SJ (2008) Lrp4 Is a receptor for agrin and forms a complex with MuSK. Cell 135:334–342
Konarev PV, Volkov VV, Sokolova AV, Koch MHJ, Svergun DI (2003) PRIMUS: a windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr 36:1277–1282
Konarev PV, Petoukhov MV, Volkov VV, Svergun DI (2006) ATSAS 2.1, a program package for small-angle scattering data analysis. J Appl Crystallogr 39:277–286
Lasker SE, Stivala SS (1966) Physicochemical studies of fractionated bovine heparin. I. Some dilute solution properties. Arch Biochem Biophys 115:360–372
Liu IH, Zhang C, Kim MJ, Cole GJ (2008) Retina development in zebrafish requires the heparan sulfate proteoglycan agrin. Dev Neurobiol 68:877–898
Malmon AG (1957) Small-angle X-ray scattering functions for ellipsoids of revolution and right circular cylinders. Acta Crystallogr 10:639–642
Mascarenhas JB, Ruegg MA, Winzen U, Halfter W, Engel J, Stetefeld J (2003) Mapping of the laminin-binding site of the N-terminal agrin domain (NtA). EMBO J 22:529–536
McFarlane AA, Stetefeld J (2009) An interdomain disulfide bridge links the NtA and first FS domain in agrin. Protein Sci 18:2421–2428
Meinen S, Barzaghi P, Lin S, Lochmuller H, Ruegg MA (2007) Linker molecules between laminins and dystroglycan ameliorate laminin-alpha2-deficient muscular dystrophy at all disease stages. J Cell Biol 176:979–993
Moll J, Barzaghi P, Lin S, Bezakova G, Lochmuller H, Engvall E, Muller U, Ruegg MA (2001) An agrin minigene rescues dystrophic symptoms in a mouse model for congenital muscular dystrophy. Nature 413:302–307
Nitkin RM, Smith MA, Magill C, Fallon JR, Yao YM, Wallace BG, McMahan UJ (1987) Identification of agrin, a synaptic organizing protein from Torpedo electric organ. J Cell Biol 105:2471–2478
O’Toole JJ, Deyst KA, Bowe MA, Nastuk MA, McKechnie BA, Fallon JR (1996) Alternative splicing of agrin regulates its binding to heparin, alpha -dystroglycan, and the cell surface. Proc Nat Acad Sci USA 93:7369–7374
Patel TR, Morris GA, Zwolanek D, Koch M, Harding SE, Stetefeld J (2010) Nano-structure of the laminin gamma-1 short arm reveals an extended and curved multidomain assembly. Matrix Biol 29:565–572
Patel TR, Besong TMD, Patel N, Meier M, Harding SE, Winzor DJ, Stetefeld J (2011a) Evidence for self-association of a miniaturized version of agrin from hydrodynamic and small-angle X-ray scattering measurements. J Phys Chem B 115:11286–11293
Patel TR, Meier M, Li J, Morris G, Rowe AJ, Stetefeld J (2011b) T-shaped arrangement of the recombinant agrin G3—IgG Fc protein. Protein Sci 20:931–940
Patel TR, Butler G, McFarlane A, Xie I, Overall CM, Stetefeld J (2012a) Site specific cleavage mediated by MMPs regulates function of agrin. PLoS One 7:e43669
Patel TR, Reuten R, Xiong S, Meier M, Winzor DJ, Koch M, Stetefeld J (2012b) Determination of a molecular shape for netrin-4 from hydrodynamic and small angle X-ray scattering measurements. Matrix Biol 31:135–140
Patel TR, Bernards C, Meier M, McEleney K, Winzor DJ, Koch M, Stetefeld J (2014) Structural elucidation of full-length nidogen and the laminin-nidogen complex in solution. Matrix Biol 33:60–67
Reist NE, Magill C, McMahan UJ (1987) Agrin-like molecules at synaptic sites in normal, denervated, and damaged skeletal muscles. J Cell Biol 105:2457–2469
Rupp F, Payan DG, Magill-Solc C, Cowan DM, Scheller RH (1991) Structure and expression of a rat agrin. Neuron 6:811–823
Schuck P (1998) Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation. Biophys J 75:1503–1512
Scotton P, Bleckmann D, Stebler M, Sciandra F, Brancaccio A, Meier T, Stetefeld J, Ruegg MA (2006) Activation of muscle-specific receptor tyrosine kinase and binding to dystroglycan are regulated by alternative mRNA splicing of agrin. J Biol Chem 281:36835–36845
Smith MA, Yao YM, Reist NE, Magill C, Wallace BG, McMahan UJ (1987) Identification of agrin in electric organ extracts and localization of agrin-like molecules in muscle and central nervous system. J Exp Biol 132:223–230
Stetefeld J, Ruegg MA (2005) Structural and functional diversity generated by alternative mRNA splicing. Trends Biochem Sci 30:515–521
Stetefeld J, Jenny M, Schulthess T, Landwehr R, Schumacher B, Frank S, Ruegg MA, Engel J, Kammerer RA (2001) The laminin-binding domain of agrin is structurally related to N-TIMP-1. Nat Struct Biol 8:705–709
Stetefeld J, Alexandrescu AT, Maciejewski MW, Jenny M, Rathgeb-Szabo K, Schulthess T, Landwehr R, Frank S, Ruegg MA, Kammerer RA (2004) Modulation of Agrin function by alternative splicing and Ca2+ binding. Structure 12:503–515
Stetefeld J, McKenna SA, Patel TR (2016) Dynamic light scattering: a practical guide and applications in biomedical sciences. Biophys Rev 8:409–427
Steubl D, Hettwer S, Vrijbloed W, Dahinden P, Wolf P, Luppa P, Wagner CA, Renders L, Heemann U, Roos M (2013) C-terminal agrin fragment–a new fast biomarker for kidney function in renal transplant recipients. Am J Nephrol 38:501–508
Sugiyama J, Bowen DC, Hall ZW (1994) Dystroglycan binds nerve and muscle agrin. Neuron 13:103–115
Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallog 25:495–503
Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76:2879–2886
Tatrai P, Dudas J, Batmunkh E, Mathe M, Zalatnai A, Schaff Z, Ramadori G, Kovalszky I (2006) Agrin, a novel basement membrane component in human and rat liver, accumulates in cirrhosis and hepatocellular carcinoma. Lab Invest 86:1149–1160
Tsen G, Halfter W, Kroger S, Cole GJ (1995) Agrin is a heparan sulfate proteoglycan. J Biol Chem 270:3392–3399
Wills PR, Comper WD, Winzor DJ (1993) Thermodynamic nonideality in macromolecular solutions: interpretation of virial coefficients. Arch Biochem Biophys 300:206–212
Wills PR, Jacobsen MP, Winzor DJ (1996) Direct analysis of solute self-association by sedimentation equilibrum. Biopolymers 38:119–130
Wilson EK, Scrutton NS, Cölfen H, Harding SE, Jacobsen MP, Winzor DJ (1997) An ultracentrifugal approach to quantitative characterization of the molecular assembly of a physiological electron-transfer complex. The interaction of electron-transferring flavoprotein with trimethylamine dehydrogenase. Eur J Biochem 243:393–399
Yphantis DA (1964) Equilibrium ultracentrifugation of dilute solutions. Biochemistry 3:297–317
Acknowledgements
TRP thanks the Canadian Institutes of Health Research for PDF. He is a Canada Research Chair in RNA and Protein Biophysics. JS holds the Canada Research Chair in Structural Biology and Biophysics. Professor Markus Ruegg kindly provided the minagrin gene.
Author information
Authors and Affiliations
Corresponding authors
Additional information
Special Issue: 23rd International AUC Workshop and Symposium.
Rights and permissions
About this article
Cite this article
Patel, T.R., Besong, T.M.D., Meier, M. et al. Interaction studies of a protein and carbohydrate system using an integrated approach: a case study of the miniagrin–heparin system. Eur Biophys J 47, 751–759 (2018). https://doi.org/10.1007/s00249-018-1291-5
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-018-1291-5